Liquid fuels can be derived from solid feedstock materials by a series of operations including treatment of the feedstock to produce a feed stream that is then treated to form the desired product fuel. For the case of biomass, treatment of the feed stream can involve fermentation reactions and/or can involve catalyzed synthesis of fuels from precursors such as hydrogen and carbon monoxide in the feed stream. The present invention provides improvements in the efficiency of production of liquid fuels from the biomass as well as coal, petroleum coke and the like.